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1. Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America

Author: Zamudio, Roxana, Boerlin, Patrick, Beyrouthy, Racha, Madec, Jean-Yves, Schwarz, Stefan, Mulvey, Michael R, Zhanel, George G, Cormier, Ashley, Chalmers, Gabhan, Bonnet, Richard, Haenni, Marisa, Eichhorn, Inga, Kaspar, Heike, Garcia-Fierro, Raquel, Wood, James LN, Mather, Alison E, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), University of Guelph, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Centre National de Référence de la Résistance aux Antibiotiques [CHU Clermont-Ferrand] (CNR), CHU Clermont-Ferrand, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Freie Universität Berlin, Veterinary Centre for Resistance Research (TZR), Free University of Berlin (FU), Public Health Agency of Canada, University of Manitoba [Winnipeg], Federal Office of Consumer Protection and Food Safety, University of Cambridge [UK] (CAM), University of East Anglia [Norwich] (UEA), This project was supported by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), through the Medical Research Council (MRC, MR/R000948/1) [R.Z., J.L.N.W., A.E.M.], the Canadian Institutes of Health Research (CFC-150770) [A.C., G.C., P.B.], and the Genomics Research and Development Initiative (Government of Canada) [M.R.M.], the German Federal Ministry of Education and Research (BMBF) grant no. 01KI1709 [I.E., H.K., S.S.], the French Agency for food environmental and occupational health & safety (Anses) [R.G.F., M.H., J.Y.M.], and the French National Reference Center (CNR) for antimicrobial resistance [R. Beyrouthy, R. Bonnet]. Support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) through the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain) [R.Z., A.E.M.]., European Project: JPI-EC-AMR, European Project: 323209,EC:FP7:HEALTH,FP7-JPROG-2012-RTD,JPIAMR(2012), Zamudio, Roxana [0000-0003-3634-4828], Schwarz, Stefan [0000-0002-6303-8212], Chalmers, Gabhan [0000-0002-6651-4253], Wood, James LN [0000-0002-0258-3188], Mather, Alison E [0000-0001-6513-3515], and Apollo - University of Cambridge Repository
Subjects: Multidisciplinary, Cephalosporin Resistance, General Physics and Astronomy, 500 Naturwissenschaften und Mathematik::570 Biowissenschaften, Biologie::570 Biowissenschaften, Biologie, General Chemistry, Antimicrobial resistance, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, beta-Lactamases, General Biochemistry, Genetics and Molecular Biology, Anti-Bacterial Agents, Cephalosporins, Bacterial genetics, Escherichia coli, Animals, Humans, Bacterial genomics, Phylogeny, Escherichia coli Infections, Plasmids
Abstract: Funder: Genomics Research and Development Initiative (Government of Canada), the German Federal Ministry of Education and Research (BMBF) grant no. 01KI1709, the French Agency for food environmental and occupational health & safety (Anses), and the French National Reference Center (CNR) for antimicrobial resistance., Extended-spectrum cephalosporins (ESCs) are critically important antimicrobial agents for human and veterinary medicine. ESC resistance (ESC-R) genes have spread worldwide through plasmids and clonal expansion, yet the distribution and dynamics of ESC-R genes in different ecological compartments are poorly understood. Here we use whole genome sequence data of Enterobacterales isolates of human and animal origin from Europe and North America and identify contrasting temporal dynamics. AmpC β-lactamases were initially more dominant in North America in humans and farm animals, only later emerging in Europe. In contrast, specific extended-spectrum β-lactamases (ESBLs) were initially common in animals from Europe and later emerged in North America. This study identifies differences in the relative importance of plasmids and clonal expansion across different compartments for the spread of different ESC-R genes. Understanding the mechanisms of transmission will be critical in the design of interventions to reduce the spread of antimicrobial resistance.
Published: 2022

2. High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods

Author: Dearbháile Morris, Gabriella Centorotola, Pascal Piveteau, Carla Rodrigues, Alessandra Cornacchia, Sylvain Brisse, Marisa Haenni, Niamh Cahill, Kathrin Hauser, Francesco Pomilio, Elodie Barbier, Eva Møller Nielsen, Malgorzata Ligowska-Marzeta, Raquel Garcia Fierro, Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Austrian Agency for Health and Food Safety (AGES), National University of Ireland [Galway] (NUI Galway), Statens Serum Institut [Copenhagen], Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise Guiseppe Caporale (IZSAM), Partenaires INRAE, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), This work was supported financially by the MedVetKlebs project, a component of European Joint Program One Health EJP, which has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 773830. C.R. was also financed by a Roux-Cantarini grant from Institut Pasteur.This research was funded, in whole or in part, by Institut Pasteur and by the European Union’s Horizon 2020 research and innovation program. For the purpose of open access, the authors have applied a CC-BY public copyright license to any author manuscript version arising from this submission., We thank James Bray and Keith Jolley for technical assistance with genomic assemblies of KpSC isolates from Ireland. We thank the Institut Pasteur teams for the curation and maintenance of BIGSdb-Pasteur databases at http://bigsdb.pasteur.fr/., and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: Microbiology (medical), Veterinary medicine, antibiotic resistance, Meat, Genotype, Physiology, Klebsiella pneumoniae, [SDV]Life Sciences [q-bio], Food Contamination, Microbial Sensitivity Tests, beta-Lactamases, Foodborne Diseases, chemistry.chemical_compound, Bacterial Proteins, Drug Resistance, Multiple, Bacterial, Genetics, culture methods, genomics, Prevalence, Animals, Humans, Colonization, One Health, Phylogeny, Genetic diversity, High prevalence, General Immunology and Microbiology, Ecology, biology, transmission, Genetic Variation, Cell Biology, Simmons' citrate agar, biology.organism_classification, food sector, Anti-Bacterial Agents, Klebsiella Infections, Europe, Food sector, Infectious Diseases, chemistry, Food products, Klebsiella pneumoniae, food sector, transmission, chicken meat, salads, antibiotic resistance, One Health, genomics, surveillance, culture methods, surveillance, Salads, chicken meat, Chickens
Abstract: Klebsiella pneumoniae species complex (KpSC) is a leading cause of multidrug-resistant human infections. To better understand the potential contribution of food as a vehicle of KpSC, we conducted a multicentric study to define an optimal culture method for its recovery from food matrices, and to characterize food isolates phenotypically and genotypically. Chicken meat (n=160) and salad (n=145) samples were collected in five European countries and screened for KpSC presence using culture-based and ZKIR qPCR methods. Enrichment using buffered peptone water followed by streaking on Simmons citrate agar with inositol (44°C/48h) was defined as the most suitable selective culture method for KpSC recovery. High prevalence of KpSC was found in chicken meat (60% and 52% by ZKIR qPCR and culture approach, respectively) and salad (30% and 21%, respectively) samples. Genomic analyses revealed high genetic diversity with the dominance of phylogroups Kp1 (91%) and Kp3 (6%). 82% of isolates presented a natural antimicrobial susceptibility phenotype and genotype, with only four CTX-M-15-producing isolates detected. Notably, identical genotypes were found across samples: same food type and same country (15 cases); different food types and same country (1); same food type and two countries (1), suggesting high rates of transmission of KpSC within the food sector. Our study provides a novel isolation strategy for KpSC from food matrices and reinforces the view of food as a potential source of KpSC colonization in humans.ImportanceBacteria of the Klebsiella pneumoniae species complex (KpSC) are ubiquitous and K. pneumoniae (Kp) is a leading cause of antibiotic-resistant infections in humans and animals. Despite the urgent public health threat represented by Kp, there is a lack of knowledge on the contribution of food sources to colonization and subsequent infection in humans. This is partly due to the absence of standardized methods for characterizing KpSC presence in food matrices. Our multicentric study provides and implements a novel isolation strategy for KpSC from food matrices and shows that KpSC members are highly prevalent in salads and chicken meat, reinforcing the view of food as a potential source of KpSC colonization in humans. Despite the large genetic diversity and the low-levels of resistance detected, the occurrence of identical genotypes across samples suggests high rates of transmission of KpSC within the food sector, which need to be further explored to define possible control strategies.
Published: 2022

3. Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance

Author: Nunez-Garcia, J., AbuOun, M., Storey, N., Brouwer, M.S., Delgado-Blas, J.F., Mo, S.S., Ellaby, N., Veldman, K.T., Haenni, M., Châtre, P., Madec, J.Y., Hammerl, J.A., Serna, C., Getino, M., La Ragione, R., Naas, T., Telke, A.A., Glaser, P., Sunde, M., Gonzalez-Zorn, B., Ellington, M.J., Anjum, M.F., Animal and Plant Health Agency [Addlestone, UK] (APHA), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Norwegian Veterinary Institute [Oslo], Public Health England [London], Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), German Federal Institute for Risk Assessment [Berlin] (BfR), University of Surrey (UNIS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Écologie et Évolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: ARDIG, Microbial Sensitivity Tests, Antimicrobial resistance, Next generation sequencing, MESH: Anti-Bacterial Agents, MESH: Drug Resistance, Bacterial, Drug Resistance, Bacterial, Escherichia coli, Life Science, Humans, MESH: High-Throughput Nucleotide Sequencing, Escherichia coli Infections, MESH: Escherichia coli Infections, Host Pathogen Interaction & Diagnostics, MESH: Microbial Sensitivity Tests, Multidisciplinary, MESH: Escherichia coli, Bacteriologie, Computational Biology, High-Throughput Nucleotide Sequencing, Bacteriology, Bacteriology, Host Pathogen Interaction & Diagnostics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Host Pathogen Interactie & Diagnostiek, Anti-Bacterial Agents, Bacteriologie, Host Pathogen Interactie & Diagnostiek, MESH: Computational Biology
Abstract: Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance (AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype–phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.
Published: 2022

4. Interplay between Bacterial Clones and Plasmids in the Spread of Antibiotic Resistance Genes in the Gut: Lessons from a Temporal Study in Veal Calves

Author: Jean-Yves Madec, Méril Massot, Bénédicte Condamine, Marisa Haenni, Pierre Châtre, Olivier Clermont, Véronique Métayer, Erick Denamur, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), INTERBEV (Protocol N° SECU-15-31), La Fondation pour la Recherche Médicale to M.M. (grant number FDM20150633309), La Fondation pour la Recherche Médicale to E.D. (équipe FRM 2016, grant number DEQ20161136698), ANR-16-JPEC-0004,TransComp-ESC-R,Genomic approach to transmission and compartmentalization of extended-spectrum cephalosporin resistance in Enterobacteriaceae from animals and humans(2016), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: clone (Java method), Context (language use), Biology, medicine.disease_cause, Applied Microbiology and Biotechnology, beta-Lactamases, Microbiology, 03 medical and health sciences, Plasmid, MESH: Plasmids, plasmid, MESH: Anti-Bacterial Agents, MESH: Drug Resistance, Bacterial, Drug Resistance, Bacterial, Escherichia coli, medicine, Animals, Colonization, Gene, Genotyping, 030304 developmental biology, clone, MESH: Red Meat, 2. Zero hunger, 0303 health sciences, Ecology, MESH: Escherichia coli, Public and Environmental Health Microbiology, 030306 microbiology, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, Clone Cells, Red Meat, Carriage, ESBL, Cattle, veal calves, Plasmids, Food Science, Biotechnology
Abstract: International audience; Intestinal carriage of extended spectrum b-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing, and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over 6 months. We characterized the bacterial clones and plasmids carrying bla ESBL genes with a combination of genotyping methods, whole genome sequencing, and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [bla CTX-M-1 (64.7%), bla CTX-M-14 (33.5%), or bla CTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and bla CTX-M-carrying plasmids, few bla CTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario "clone versus plasmid spread" depended on the farm. Thus, epistatic interactions between resistance genes, plasmids, and bacterial clones contribute to optimize fitness in specific environments. IMPORTANCE The gut microbiota is the epicenter of the emergence of resistance. Considerable amount of knowledge on the molecular mechanisms of resistance has been accumulated, but the ecological and evolutionary forces at play in nature are less studied. In this context, we performed a field work on temporal intestinal carriage of extended spectrum b-lactamase (ESBL)-producing Escherichia coli in veal farms. Veal calves are animals with one of the highest levels of ESBL producing E. coli fecal carriage, due to early high antibiotic exposure. We were able to show that calves were colonized successively by different ESBL-producing E. coli clones, and that two main scenarios were at play in the spread of bla CTX-M genes among calves: efficient colonization of several calves by a few bacterial clones and successful plasmid spread in various bacterial clones. Such knowledge should help develop new strategies to fight the emergence of antibiotic-resistance.
Published: 2021

5. Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota

Author: Rochegüe, Tony, Haenni, Marisa, Mondot, Stanislas, Astruc, Chloé, Cazeau, Géraldine, Ferry, Tristan, Madec, Jean-Yves, Lupo, Agnese, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de Lyon, Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, 3C-G Clinical, Unité Epidémiologie et Appui à la Surveillance (EAS), Service des Maladies Infectieuses et Tropicales [Lyon], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-11-LABX-0048,ECOFECT,Dynamiques eco-évolutives des maladies infectieuses(2011), and ANR-11-IDEX-0007,Avenir L.S.E.,PROJET AVENIR LYON SAINT-ETIENNE(2011)
Subjects: intestinal microbiota, dogs, macrolides, beta-lactams, poultry, Veterinary medicine, cats, food-producing animals, pigs, Review, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, QL1-991, SF600-1100, companion animals, fluoroquinolones, bacitracin, bovines, Zoology, horses, tetracycline
Abstract: Simple Summary Antibiotics perturb the gastrointestinal microbiota by killing bacteria beneficial for animal health and favoring the emergence of potential pathogens. Furthermore, antibiotics favor the emergence of resistant bacteria. Current knowledge on animals’ intestinal microbiota and effects of antibiotics is blurred by the various posology, administration routes, and implemented methodologies for its analysis. We summarized 71 studies analyzing the administration of antibiotics by different routes, conducted on the main food-producing and companion animals, highlighting differences in the methodology applied for the intestinal microbiota and antibiotic resistance analysis. Overall, therapeutic dosage decreased bacterial species diversity and richness in the microbiota and selected antibiotic resistance genes. For non-therapeutic dosage, information on the selection of antibiotic resistance was scarce and the effect on the intestinal microbiota scattered. Understanding the gut microbiota composition and function in animals could open up strategies for its modulation to improve animal health and performance, and to minimize the negative impact of antibiotics. Abstract Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals’ health status, with positive consequences on global health.
Published: 2021

6. Host Colonization as a Major Evolutionary Force Favoring the Diversity and the Emergence of the Worldwide Multidrug-Resistant Escherichia coli ST131

Author: Guillaume Dalmasso, Richard Bonnet, Marisa Haenni, Racha Beyrouthy, Jean-Yves Madec, Marie-Hélène Nicolas-Chanoine, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Centre National de Référence de la Résistance aux Antibiotiques [CHU Clermont-Ferrand] (CNR), CHU Clermont-Ferrand, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, JPIAMR program TransComp-ESC-R, and ANR-16-JPEC-0002,ST131TS,Escherichia coli ST131: a model for high-risk transmission dynamics of antimicrobial resistance(2016)
Subjects: Male, antibiotic resistance, ST131, Virulence Factors, extended-spectrum beta-lactamase, Virulence, Population genetics, Biology, MESH: Genome, Bacterial, medicine.disease_cause, Global Health, Genome, Microbiology, Birds, Evolution, Molecular, one health, Mice, Dogs, Virology, Drug Resistance, Multiple, Bacterial, medicine, Escherichia coli, Animals, Humans, Evolutionary dynamics, MESH: Evolution, Molecular, veterinary microbiology, Escherichia coli Infections, genome analysis, Disease Reservoirs, Genetics, MESH: Disease Reservoirs, MESH: Escherichia coli, Host (biology), host colonization, veterinary epidemiology, population genetics, population structure, MESH: Drug Resistance, Multiple, Bacterial, Pathogenicity island, QR1-502, virulence, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Host-Pathogen Interactions, extended-spectrum betalactamase, Adaptation, Genome, Bacterial, Research Article
Abstract: International audience; The emergence of multidrug-resistant Escherichia coli ST131 is a major worldwide public health problem in humans. According to the "one health" approach, this study investigated animal reservoirs of ST131, their relationships with human strains, and the genetic features associated with host colonization. High-quality genomes originating from human, avian, and canine hosts were classified on the basis of their accessory gene content using pangenomic. Pangenomic clusters and subclusters were specifi- cally and significantly associated with hosts. The functions of clustering accessory genes were mainly enriched in functions involved in DNA acquisition, interactions, and virulence (e.g., pathogenesis, response to biotic stimulus and interaction between organisms). Accordingly, networks of cooccurrent host interaction factors were significantly associated with the pangenomic clusters and the originating hosts. The avian strains exhibited a specific content in virulence factors. Rarely found in humans, they corresponded to pathovars responsible for severe human infections. An emerging subcluster significantly associated with both human and canine hosts was evidenced. This ability to significantly colonize canine hosts in addition to humans was associated with a specific content in virulence factors (VFs) and metabolic functions encoded by a new pathogenicity island in ST131 and an improved fitness that is probably involved in its emergence. Overall, VF content, unlike the determinants of antimicrobial resistance, appeared as a key actor of bacterial host adaptation. The host dimension emerges as a major driver of genetic evolution that shapes ST131 genome, enhances its diversity, and favors its dissemination.IMPORTANCE Until now, there has been no indication that the evolutionary dynamics of Escherichia coli ST131 may reflect independent and host-specific adaptation of this lineage outside humans. In contrast, the limited number of ST131 reports in animals supported the common view that it rather reflects a spillover of the human sector. This study uncovered a link between host, ST131 population structure, and virulence factor content which appeared to reflect adaptation to hosts. This study helps to better understand the reservoir of ST131, the putative transmission flux, associated risks and the evolutionary dynamics of this bacterial population and highlights a paradigm in which host colonization stands as a key ecological force of the ST131 evolution.
Published: 2021

7. Drivers of ESBL-producing Escherichia coli dynamics in calf fattening farms: A modelling study

Author: Laura Temime, Lulla Opatowski, Philippe Glaser, Jean-Yves Madec, Jonathan Bastard, Marisa Haenni, Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials (EMAE), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Université Paris Diderot, Sorbonne Paris Cité, Paris, France, Université Paris Diderot - Paris 7 (UPD7), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was supported by the INCEPTION project (PIA/ANR-16-CONV-0005) to JB, by internal resources of Institut Pasteur, the French National Institute of Health and Medical Research (Inserm) and the University of Versailles Saint-Quentin-en-Yvelines (UVSQ), by the French Government 'Investissement d'Avenir' program Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant ANR-10-LABX-62-IBEID) and by the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No. 773830 (Project ARDIG, EJP One Health), the TransComp-ESC-R AAP JPI-EC-AMR and INTERBEV (Protocol N° SECU-15-31)., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health)(2018), Temime, Laura, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Klebsiella pneumoniae: from ecology to source attribution and transmission control - MedVetKlebs (a component of European Joint Programme One Health) - - H2020-SFS-2017-12018-01-01 - 2019-12-31 - 773830 - VALID, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health EJP)(2018)
Subjects: Medicine (General), Veterinary medicine, Livestock, 030231 tropical medicine, Esbl production, Calves, Biology, Antimicrobial resistance, medicine.disease_cause, law.invention, 03 medical and health sciences, R5-920, 0302 clinical medicine, Antibiotic resistance, [STAT.AP] Statistics [stat]/Applications [stat.AP], law, Escherichia coli, Credible interval, medicine, 030212 general & internal medicine, 030304 developmental biology, 2. Zero hunger, [STAT.AP]Statistics [stat]/Applications [stat.AP], 0303 health sciences, Mathematical modelling, 030306 microbiology, business.industry, Public Health, Environmental and Occupational Health, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, ESBLLivestock, Infectious Diseases, Antimicrobial use, Transmission (mechanics), Carriage, ESBL, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, business, Research Paper
Abstract: The contribution of bacteria in livestock to the global burden of antimicrobial resistance raises concerns worldwide. However, the dynamics of selection and diffusion of antimicrobial resistance in farm animals are not fully understood. Here, we used veal calf fattening farms as a model system, as they are a known reservoir of Extended Spectrum β-Lactamase-producing Escherichia coli (ESBL-EC). Longitudinal data of ESBL-EC carriage and antimicrobial use (AMU) were collected from three veal calf farms during the entire fattening process. We developed 18 agent-based mechanistic models to assess different hypotheses regarding the main drivers of ESBL-EC dynamics in calves. The models were independently fitted to the longitudinal data using Markov Chain Monte Carlo and the best model was selected. Within-farm transmission between individuals and sporadic events of contamination were found to drive ESBL-EC dynamics on farms. In the absence of AMU, the median carriage duration of ESBL-EC was estimated to be 19.6 days (95% credible interval: [12.7; 33.3]). In the best model, AMU was found to influence ESBL-EC dynamics, by affecting ESBL-EC clearance rather than acquisition. This effect of AMU was estimated to decrease gradually after the end of exposure and to disappear after 62.5 days [50.0; 76.9]. Moreover, using a simulation study, we quantified the efficacy of ESBL-EC mitigation strategies. Decreasing ESBL-EC prevalence by 50% on arrival at the fattening farm reduced prevalence at slaughter age by 33.3%. Completely eliminating the use of selective antibiotics had a strong effect on average ESBL-EC prevalence (relative reduction of 79.6%), but the effect was mild if this use was only decreased by 50% compared to baseline (relative reduction of 3.7%).
Published: 2021

8. Comparison of Phenotypical Antimicrobial Resistance between Clinical and Non-Clinical E. coli Isolates from Broilers, Turkeys and Calves in Four European Countries

Author: Agnès Perrin-Guyomard, Octavio Mesa-Varona, Martina Velasova, Bernd-Alois Tenhagen, Mirjam Grobbel, Muna F. Anjum, Heike Kaspar, Sophie A. Granier, Madelaine Norström, Eric Jouy, R. Mader, Jean-Yves Madec, Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Unité Antibiorésistance et Virulence Bactériennes, Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal and Plant Health Agency [Addlestone, UK] (APHA), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Norwegian Veterinary Institute [Oslo], Federal Office of Consumer Protection and Food Safety, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], This work was carried out within the framework of the ARDIG project, the European Joint Programme (EJP) on AMU and AMR in humans, food and animals. ARDIG project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No 773830., European Project: 773830, Unité Antibiorésistance et Virulence Bactériennes (AVB), Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: 0301 basic medicine, Veterinary medicine, dinde, antibiotic resistance, Nalidixic acid, résistance aux antibiotiques, veterinary drug, E. coli, Ampicillin, AMR, animal, bacteria, lcsh:QH301-705.5, agriculture, bactérie, veau, Antimicrobial, 3. Good health, Europe, phénotype, Gentamicin, Livestock, medicine.drug, Microbiology (medical), médicament vétérinaire, Tetracycline, clinical isolates, 030106 microbiology, poulet, Biology, broiler, Article, 03 medical and health sciences, Antibiotic resistance, résistance aux antimicrobiens, Virology, phentoype, medicine, Escherichia coli, turkey, antimicrobial resistance, microbiologie, calf, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, business.industry, microbiology, Broiler, élevage, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, livestock, 030104 developmental biology, lcsh:Biology (General), non-clinical isolates, business
Abstract: International audience; Livestock data on antimicrobial resistance (AMR) are commonly collected from bacterial populations of clinical and non-clinical isolates. In contrast to data on non-clinical isolates from livestock, data on clinical isolates are not harmonized in Europe. The Normalized Resistance Interpretation (NRI) method was applied to overcome the lack of harmonization of laboratory methods and interpretation rules between monitoring systems. Statistical analyses were performed to identify associations between the isolate type (clinical vs. non-clinical) and resistance to four antimicrobials (ampicillin, tetracycline, gentamicin, and nalidixic acid) per animal category in Germany and France. Additional statistical analyses comparing clinical and non-clinical isolates were performed with the available data on the same antimicrobial panel and animal categories from the UK and Norway. Higher resistance prevalence was found in clinical isolates compared to non-clinical isolates from calves to all antimicrobials included in Germany and France. It was also found for gentamicin in broilers from France. In contrast, in broilers and turkeys from Germany and France and in broilers from the UK, a higher resistance level to ampicillin and tetracycline in non-clinical isolates was encountered. This was also found in resistance to gentamicin in isolates from turkeys in Germany. Resistance differed within countries and across years, which was partially in line with differences in antimicrobial use patterns. Differences in AMR between clinical and non-clinical isolates of Escherichia coli are associated with animal category (broiler, calf, and turkey) and specific antimicrobials. The NRI method allowed comparing results of non-harmonized AMR systems and might be useful until international harmonization is achieved.
Published: 2021

9. Characterization of cultivable airborne bacteria and their antimicrobial resistance pattern in French milking parlour

Author: Jean-Yves Madec, Véronique Métayer, Marisa Haenni, Charlotte Valat, Janick Rocher, Frédéric Laurent, Antoine Drapeau, Sandrine Bayle, Laboratoire des Sciences des Risques (LSR), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Saint-Christol (SAINT-CHRISTOL), Institut National de la Recherche Agronomique (INRA), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: Veterinary medicine, medicine.drug_class, Antibiotic resistance, Health, Toxicology and Mutagenesis, Antibiotics, Indoor bioaerosol, 010501 environmental sciences, Opportunist pathogen, medicine.disease_cause, 01 natural sciences, Milking parlour, Milking, [SPI]Engineering Sciences [physics], medicine, Environmental Chemistry, 0105 earth and related environmental sciences, biology, Pathogenic bacteria, General Medicine, Bovine, Acinetobacter, biology.organism_classification, Pollution, Aerococcus, Airborne, Particulate matter, Bacteria
Abstract: International audience; The main goal of this preliminary study was to quantify airborne particles and characterize the dominant cultivable bacterial species as well as some Gram-positive species, and their antibiotic resistance pattern, from environmental samples taken inside and outside of a dairy milking parlour. Sampling was performed over 2 days, in different seasons. The small viable particulate matter < 10 μm (bioaerosols) and cultivable bacteria reached their highest concentrations in the milking parlour. The majority of airborne bacteria in the milking parlour belonged to the genera Staphylococcus (41.9%) and Bacillus (20.9%). A total of 32 different bacterial species of Staphylococcus, Aerococcus, Bacillus, Pseudomonas, Serratia and Acinetobacter were identified. Many of these bacteria may be opportunistic pathogens, causing disease in humans or animals. We found low levels of acquired resistance to the antibiotics commonly used in human or animal infections caused by these opportunistic bacteria. More specifically, resistance to tetracyclines (13.4%), penicillin G (13.4%) and macrolides (7.5%) was identified in Staphylococcus sp. as was a methicillin-resistant S. hominis and resistance to spiramycin (n = 1), lincomycin (n = 1) and streptomycin (n = 2) in Aerococcus sp. An assessment of the occupational risk run by dairy farmers for contracting infections after long- or short-term exposure to micro-organisms requires further studies on the concentration of opportunistic pathogenic bacteria in dairy farm environments.
Published: 2021

10. Horsing around : Escherichia coli ST1250 of equine origin harboring epidemic IncHI1/ST9 plasmid with blaCTX-M-1and an operon for short-chain fructooligosaccharide metabolism

Author: Valcek, Adam, Sismova, Petra, Nesporova, Kristina, Overballe-Petersen, Søren, Bitar, Ibrahim, Jamborova, Ivana, Kant, Arie, Hrabak, Jaroslav, Wagenaar, Jaap A, Madec, Jean-Yves, Damborg, Peter, van Duijkeren, Engeline, Ewers, Christa, Hordijk, Joost, Hasman, Henrik, Brouwer, Michael S M, Dolejska, Monika, Klinische infectiologie en microb. lab., dI&I I&I-4, University of Veterinary and Pharmaceutical Sciences [Brno] (VFU), Statens Serum Institut [Copenhagen], First Faculty of Medicine Charles University [Prague], Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Utrecht University [Utrecht], Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018), Department of Bio-engineering Sciences, Klinische infectiologie en microb. lab., and dI&I I&I-4
Subjects: Operon, Epidemiology, Bioinformatica & Diermodellen, Virulence, Biology, Multidrug resistance, medicine.disease_cause, Genome, Epidemiology and Surveillance, 03 medical and health sciences, Plasmid, Bio-informatics & Animal models, ST1250, medicine, Escherichia coli, Escherichia coli, IncHI1, ST1250, horses, multidrug resistance, plasmids, Epidemiology, Bio-informatics & Animal models, Pharmacology (medical), Replicon, Horses, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, Pharmacology, Host Pathogen Interaction & Diagnostics, Epidemiologie, 0303 health sciences, 030306 microbiology, Bacteriologie, Bacteriology, Bacteriology, Host Pathogen Interaction & Diagnostics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Host Pathogen Interactie & Diagnostiek, 3. Good health, Multiple drug resistance, Infectious Diseases, Epidemiologie, Bioinformatica & Diermodellen, Bacteriologie, Host Pathogen Interactie & Diagnostiek, IncHI1, Plasmids
Abstract: The relatedness of the equine-associated Escherichia coli strain ST1250 and its single- and double-locus variants (ST1250-SLV/DLV), obtained from horses in Europe, was studied by comparative genome analysis. A total of 54 isolates of E. coli ST1250 and ST1250-SLV/DLV from healthy and hospitalized horses across Europe (Czech Republic [n = 23], The Netherlands [n = 18], Germany [n = 9], Denmark [n = 3], and France [n = 1]) from 2008 to 2017 were subjected to whole-genome sequencing. An additional 25 draft genome assemblies of E. coli ST1250 and ST1250- SLV/DLV were obtained from the public databases. The isolates were compared for genomic features, virulence genes, clade structure, and plasmid content. The complete nucleotide sequences of eight IncHI1/ST9 plasmids and one IncHI1/ST2 plasmid were obtained using long-read sequencing by PacBio or MinION. In the collection of 79 isolates, only 10 were phylogenetically close (,8 single nucleotide polymorphisms [SNP]). The majority of isolates belonged to phylogroup B1 (73/79 [92.4%]) and carried blaCTX-M-1 (58/79 [73.4%]). The plasmid content of the isolates was dominated by IncHI1 of ST9 (56/62 [90.3%]) and ST2 (6/62 [9.7%]), while 84.5% (49/58) of the blaCTX-M-1 genes were associated with the presence of the IncHI1 replicon of ST9 and 6.9% (4/58) with the IncHI1 replicon of ST2 within the corresponding isolates. The operon for the utilization of short-chain fructooligosaccharides (the fos operon) was present in 55 of 79 (69.6%) isolates, and all of these carried IncHI1/ST9 plasmids. The eight complete IncHI1/ST9 plasmid sequences showed the presence of blaCTX-M-1 and the fos operon within the same molecule. Sequences of IncHI1/ST9 plasmids were highly conserved (.98% similarity) regardless of country of origin and differed only in the structure and integration site of the multidrug resistance (MDR) region. E. coli ST1250 and ST1250-SLV/DLV are phylogenetically diverse strains associated with horses. A strong linkage of E. coli ST1250 with the epidemic multidrug resistance plasmid lineage IncHI1/ST9 carrying blaCTX-M-1 and the fos operon was identified.
Published: 2021

11. Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli

Author: Rafael Patiño-Navarrete, Lauraine Gauthier, Julie Takissian, Nicolas Cabanel, Isabelle Rosinski-Chupin, Rémy A. Bonnin, Monzer Hamze, Philippe Glaser, Jean-Yves Madec, Thierry Naas, Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Université Paris-Sud - Paris 11 (UP11)-Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence Associé de la Résistance aux Antibiotiques [Hôpital Bicêtre AP-HP] (CNRARA/Service de Microbiologie), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Hôpital Bicêtre, Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Libanaise, This work was supported by grants from the French National Research Agency (ANR LabEx IBEID and ANR-10-LABX-33), from the Joint Program Initiative on Antimicrobial Resistance (ANR-14-JAMR-0002), and from the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreement No. 773830 (Project ARDIG, EJP One Health), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health)(2018), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence Associé de la Résistance aux Antibiotiques, Hôpital Bicêtre-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11), Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health EJP)(2018)
Subjects: 0301 basic medicine, Penicillin binding proteins, lcsh:Medicine, Multidrug resistance, medicine.disease_cause, Genome, Bacterial evolution, Enteropathogenic Escherichia coli, Shigella, Genetics (clinical), Phylogeny, Genetics, 0303 health sciences, Escherichia coli Proteins, Porin, Multidrug resistance bacteria, Enterobacteriaceae, Phenotype, 3. Good health, Molecular Medicine, Penicillin-binding proteins, Porine, Lineage (genetic), lcsh:QH426-470, Gene Transfer, Horizontal, 030106 microbiology, Porins, Biology, beta-Lactam Resistance, beta-Lactamases, Lateral gene transfers, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, Phylogenetics, medicine, Allele, Molecular Biology, Gene, Escherichia coli, 030304 developmental biology, Molecular epidemiology, 030306 microbiology, Research, lcsh:R, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, lcsh:Genetics, 030104 developmental biology, Carbapenems, Mutation, Peptidoglycan Glycosyltransferase
Abstract: Background Carbapenem-resistant Enterobacteriaceae are considered by WHO as “critical” priority pathogens for which novel antibiotics are urgently needed. The dissemination of carbapenemase-producing Escherichia coli (CP-Ec) in the community is a major public health concern. However, the global molecular epidemiology of CP-Ec isolates remains largely unknown as well as factors contributing to the acquisition of carbapenemase genes. Methods We first analyzed the whole-genome sequence and the evolution of the E. coli sequence type (ST) 410 and its disseminated clade expressing the carbapenemase OXA-181. We reconstructed the phylogeny of 19 E. coli ST enriched in CP-Ec and corresponding to a total of 2026 non-redundant isolates. Using the EpiCs software, we determined the significance of the association between specific mutations and the acquisition of a carbapenemase gene and the most probable order of events. The impact of the identified mutations was assessed experimentally by genetic manipulations and phenotypic testing. Results In 13 of the studied STs, acquisition of carbapenemase genes occurred in multidrug-resistant lineages characterized by a combination of mutations in ftsI encoding the penicillin-binding protein 3 and in the porin genes ompC and ompF. Mutated ftsI genes and a specific ompC allele related to that from ST38 inducing reduced susceptibility to diverse β-lactams spread across the species by recombination. We showed that these mutations precede in most cases the acquisition of a carbapenemase gene. The ompC allele from ST38 might have contributed to the selection of CP-Ec disseminated lineages within this ST. On the other hand, in the pandemic ST131 lineage, CP-Ec were not associated with mutations in ompC or ftsI and show no signs of dissemination. Conclusions Lineages of CP-Ec have started to disseminate globally. However, their selection is a multistep process involving mutations, recombination, acquisition of antibiotic resistance genes, and selection by β-lactams from diverse families. This process did not yet occur in the high-risk lineage ST131.
Published: 2020

12. Temporal dynamics of the fecal microbiota in veal calves in a 6-month field trial

Author: Massot, Méril, Haenni, Marisa, Nguyen, Thu Thuy, Madec, Jean-Yves, Mentré, France, Denamur, Erick, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Département d'épidémiologie, biostatistique et recherche clinique, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire de Génétique Moléculaire [Hôpital Bichat], AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Interbev Protocol N° SECU-15-31, La Fondation pour la Recherche Médicale grant number FDM20150633309, La Fondation pour la Recherche Médicale grant number DEQ20161136698, and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: 2. Zero hunger, Veal calves, lcsh:Veterinary medicine, Milk powder, Antibiotics, Escherichia coli, lcsh:QR1-502, lcsh:SF600-1100, Fecal microbiota development, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 16S rRNA gene sequencing, lcsh:Microbiology, Research Article
Abstract: Background Little is known about maturation of calves’ gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of collective antibiotic treatment in feed is common. We conducted a field study on 45 calves starting seven days after their arrival in three veal farms. We collected monthly fecal samples over six months and performed 16S rRNA gene sequencing and quantitative PCR of Escherichia coli to follow the dynamics of their microbiota, including that of their commensal E. coli populations. We used mixed-effect models to characterize the dynamics of α-diversity indices and numbers of E. coli, and searched for an effect of collective antibiotic treatments on the estimated parameters. On two farms, we also searched for associations between recommended daily doses of milk powder and bacterial abundance. Results There was high heterogeneity between calves’ microbiota upon their arrival at the farms, followed by an increase in similarity, starting at the first month. From the second month, 16 genera were detected at each sampling in all calves, representing 67.5% (± 9.9) of their microbiota. Shannon diversity index showed a two-phase increase, an inflection occurring at the end of the first month. Calves receiving antibiotics had a lower intercept estimate for Shannon index (-0.17 CI95%[0.27; -0.06], p = 0.003) and a smaller number of E. coli/ gram of feces during the treatment and in the 15 days following it (-0.37 log10 (E. coli/g) CI95%[-0.66; -0.08], p = 0.01) than unexposed calves. There were moderate to strong positive associations between the dose of milk powder and the relative abundances of the genera Megasphaera, Enterococcus, Dialister and Mitsuokella, and the number of E. coli (rs ≥ 0.40; Bonferroni corrected p < 0.05).Conclusions This observational study shows early convergence of the developing microbiota between veal calves and associations between the dose of milk powder and members of their microbiota. It suggests that administration of collective antibiotic treatment results in a reduction of diversity and size of the E. coli population and highlights the need for additional work to fully understand the impact of antibiotic treatment in the veal industry.
Published: 2020

13. A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales

Author: Pierre Bogaerts, Marisa Haenni, Elodie Couvé-Deacon, Rémy A. Bonnin, Jean-Yves Madec, Olivier Barraud, Lauraine Gauthier, Nicolas Fortineau, Philippe Glaser, Gaelle Cuzon, Laurent Dortet, Agnès B Jousset, Delphine Girlich, Thierry Naas, Youri Glupczynski, Team Resist [Le Kremlin-Bicêtre], Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae [Le Kremlin-Bicêtre], Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Bacteriology-Hygiene unit [Le Kremlin-Bicêtre], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), CHU UCL Namur, Unité Antibiorésistance et Virulence Bactériennes, Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Anti-infectieux : supports moléculaires des résistances et innovations thérapeutiques (RESINFIT), CHU Limoges-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), This work was partially funded by the University Paris-Sud, France. LD, TN and RAB are members of the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency (ANR-10-LABX-33) and by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL [ANR-14-JAMR-002]., We want to thanks Pasteur International Bioressources Networking (PibNet, Paris, France) for providing whole genome sequencing facilities. We would like to thank the Transposon Registry for transposon nomenclature (https://transposon.lstmed.ac.uk/tn-registry). We thank INTEGRALL database for integron and gene cassette nomenclatures., ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), Université Paris-Sud - Paris 11 (UP11)-Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Unité Antibiorésistance et Virulence Bactériennes (AVB), Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), UCL - (MGD) Laboratoire de biologie clinique, UCL - SSS/IREC/MONT - Pôle Mont Godinne, Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Bodescot, Myriam, Research Laboratory on Drugs and Therapeutic Innovation - - LERMIT2010 - ANR-10-LABX-0033 - LABX - VALID, and programmation conjointe européenne sur la résistance antimicrobienne - Structure-guided design of pan inhibitors of metallo-ß-lactamases - - DesInMBL2014 - ANR-14-JAMR-0002 - JPI AMR - VALID
Subjects: DNA, Bacterial, 0301 basic medicine, clone (Java method), Lineage (genetic), Science, 030106 microbiology, Antimicrobial resistance, beta-Lactamases, Article, 03 medical and health sciences, Plasmid, Bacterial Proteins, Belgium, Recombinase, polycyclic compounds, Animals, Humans, Clinical microbiology, Proteus mirabilis, Gene, Genetics, Multidisciplinary, biology, Phylogenetic tree, integumentary system, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Chromosomes, Bacterial, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, 030104 developmental biology, Composite transposon, Genes, Bacterial, DNA Transposable Elements, bacteria, Medicine, France, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Plasmids
Abstract: In Enterobacterales, the most common carbapenemases are Ambler’s class A (KPC-like), class B (NDM-, VIM- or IMP-like) or class D (OXA-48-like) enzymes. This study describes the characterization of twenty-four OXA-23 or OXA-58 producing-Proteus mirabilis isolates recovered from human and veterinary samples from France and Belgium. Twenty-two P. mirabilis isolates producing either OXA-23 (n = 21) or OXA-58 (n = 1), collected between 2013 and 2018, as well as 2 reference strains isolated in 1996 and 2015 were fully sequenced. Phylogenetic analysis revealed that 22 of the 24 isolates, including the isolate from 1996, belonged to a single lineage that has disseminated in humans and animals over a long period of time. The blaOXA-23 gene was located on the chromosome and was part of a composite transposon, Tn6703, bracketed by two copies of IS15∆II. Sequencing using Pacbio long read technology of OXA-23-producing P. mirabilis VAC allowed the assembly of a 55.5-kb structure encompassing the blaOXA-23 gene in that isolate. By contrast to the blaOXA-23 genes, the blaOXA-58 gene of P. mirabilis CNR20130297 was identified on a 6-kb plasmid. The acquisition of the blaOXA-58 gene on this plasmid involved XerC-XerD recombinases. Our results suggest that a major clone of OXA-23-producing P. mirabilis is circulating in France and Belgium since 1996.
Published: 2020

14. Scarless Removal of Large Resistance Island AbaR Results in Antibiotic Susceptibility and Increased Natural Transformability in Acinetobacter baumannii

Author: Anne-Sophie, Godeux, Elin, Svedholm, Agnese, Lupo, Marisa, Haenni, Samuel, Venner, Maria-Halima, Laaberki, Xavier, Charpentier, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Unité Antibiorésistance et Virulence Bactériennes, Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité Antibiorésistance et Virulence Bactériennes (AVB), Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE)
Subjects: Acinetobacter baumannii, Islands, Genomic Islands, Drug Resistance, Multiple, Bacterial, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents
Abstract: International audience; With a great diversity in gene composition, including multiple putative antibiotic resistance genes, AbaR islands are potential contributors to multidrug resistance in Acinetobacter baumannii. However, the effective contribution of AbaR to antibiotic resistance and bacterial physiology remains elusive. To address this, we sought to accurately remove AbaR islands and restore the integrity of their insertion site. To this end, we devised a versatile scarless genome editing strategy. We performed this genetic modification in two recent A. baumannii clinical strains: the strain AB5075 and the nosocomial strain AYE, which carry AbaR11 and AbaR1 islands of 19.7 kbp and 86.2 kbp, respectively. Antibiotic susceptibilities were then compared between the parental strains and their AbaR-cured derivatives. As anticipated by the predicted function of the open reading frame (ORF) of this island, the antibiotic resistance profiles were identical between the wild type and the AbaR11-cured AB5075 strains. In contrast, AbaR1 carries 25 ORFs, with predicted resistance to several classes of antibiotics, and the AYE AbaR1-cured derivative showed restored susceptibility to multiple classes of antibiotics. Moreover, curing of AbaRs restored high levels of natural transformability. Indeed, most AbaR islands are inserted into the comM gene involved in natural transformation. Our data indicate that AbaR insertion effectively inactivates comM and that the restored comM is functional. Curing of AbaR consistently resulted in highly transformable and therefore easily genetically tractable strains. Emendation of AbaR provides insight into the functional consequences of AbaR acquisition.
Published: 2020

15. An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes

Author: Tristan Ferry, Jean-Yves Madec, Géraldine Cazeau, Agnese Lupo, Tony Rochegüe, Véronique Métayer, Marisa Haenni, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Service des Maladies Infectieuses et Tropicales [Lyon], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), Genotyping, TaqMan, 030106 microbiology, Computational biology, Biology, Real-Time Polymerase Chain Reaction, beta-Lactamases, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, Antibiotic resistance, Enterobacteriaceae, 16S rDNA, RNA, Ribosomal, 16S, Enterobacterales, Drug Resistance, Bacterial, Screening tool, 030212 general & internal medicine, Hydrolysis, Gene Expression Regulation, Bacterial, General Medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, Infectious Diseases, blaCTX-M, blaOXA, mcr1-3, Antibiotic resistance genes
Abstract: International audience; Early antibiotic resistance determinants (ARDs) detection in humans or animals is crucial to counteract theirpropagation. The ARDs quantification is fundamental to understand the perturbation caused by disruptors,such as antibiotics, during therapies. Forty-three qPCRs on the most diffused ARDs and integrons amonghuman and animal Enterobacterales, and one on the 16S rDNA for bacteria quantification, were developed.The qPCRs, using hydrolysis probes, operated with a unique amplification condition and were tested analyticallyand diagnostically performing 435 reactions on five positive and negative controls for each qPCR. Diagnosticsensitivity and specificity were confirmed by PCR and genome sequencing of control isolates,demonstrating 100% performance for all qPCRs. An easy and rapid discrimination method for the epidemiologicallyrelevant blaCTX-Ms is provided. This large, noncommercial qPCRs inventory could serve for precisequantification of ARDs, but also as a rapid screening tool for surveillance purposes, providing the basis forfurther high-throughput developments.
Published: 2021

16. Persistence and Diffusion of mecC-Positive CC130 MRSA Isolates in Dairy Farms in Meurthe-et-Moselle County (France)

Author: Jacques Bietrix, Camille Kolenda, Anaïs Sapin, Marisa Haenni, Jean-Yves Madec, Michèle Bes, Céline Dupieux, Jason Tasse, Fréderic Laurent, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Clinique vétérinaire de l'arche, Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre National de Reference des Staphylocoques, Institut des Sciences Pharmaceutiques et Biologiques (ISPB), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon
Subjects: Microbiology (medical), Veterinary medicine, Staphylococcus aureus, lcsh:QR1-502, Biology, medicine.disease_cause, Microbiology, lcsh:Microbiology, Persistence (computer science), Milking, Agar plate, 03 medical and health sciences, methicillin resistance, Multiplex polymerase chain reaction, medicine, Dairy cattle, Original Research, 030304 developmental biology, carriage, 0303 health sciences, milk, 030306 microbiology, mecC, SCCmec, dairy cow, biochemical phenomena, metabolism, and nutrition, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Carriage
Abstract: Background: Methicillin resistance in Staphylococcus aureus (MRSA) is classically conferred by the acquisition of the mecA gene encoding an additional penicillin binding protein with low affinity for beta-lactams. A mecA variant, named mecC, was described in 2011. MRSA isolates harboring mecC of both animal and human origin have since been collected in different European countries. In France, animal cases were reported in 4 dairy farms between 2008 and 2013 in the Meurthe-et-Moselle county, all located in a 30 km perimeter, suggesting a possible dissemination of mecC-positive MRSA strains. We performed a prospective study to evaluate the local epidemiology of such strains in terms of (i) dissemination among animals, humans and in the environment, and (ii) persistence in Meurthe-et-Moselle dairy cattle farms. Methods: The 4 French dairy farms with previous reports of mecC-positive MRSA strains and 14 farms in the same perimeter were included in this study. In each farm, nasal swabs, rectal swabs and milk samples were collected from 10 randomly selected cows, as well as nasal samples from family pets, volunteer farmers and veterinarians. One farm (E0), in which mecC-MRSA isolates were detected, was selected to study more deeply the dissemination of mecC-positive strains within the farm. After pre-enrichment of swabs and milk, they were subcultured on MSSA/MRSA chromogenic selective agar plates. S. aureus colonies were tested with a multiplex PCR to detect the mecA and mecC genes. The mecC-positive strains were characterized using DNA microarray. Results: mecC-positive strains were recovered in four farms, corresponding to the ones with previous reports of mecC-positive MRSA strains, and originated only from dairy cow samples. The screening in the E0 farm showed that 22% of the dairy cows carried mecC-positive MRSA. Three strains were also isolated from the environmental samples. All mecC-positive strains belonged to the clonal complex CC130 and harbored the same spa-type t1736. Conclusion: This study found that mecC-positive MRSA isolates are able to persist within the same farms for several years after being introduced in this setting and are able to widely disseminate but only among dairy cows suggesting that milking machines might be a key player.
Published: 2019

17. Evolution of the Population Structure of Staphylococcus pseudintermedius in France

Author: Marine Bergot, Patricia Martins-Simoes, Hélène Kilian, Pierre Châtre, Kate A. Worthing, Jacqueline M. Norris, Jean-Yves Madec, Frédéric Laurent, Marisa Haenni, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Centre National de Reference des Staphylocoques, Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Sydney School of Veterinary Science, Faculty of Science, The University of Sydney -The University of Sydney, The Peter Doherty Institute for Infection and Immunity [Melbourne], University of Melbourne-The Royal Melbourne Hospital, and Santé Publique France
Subjects: 0301 basic medicine, Microbiology (medical), ST496, Staphylococcus pseudintermedius, Lineage (genetic), Population, lcsh:QR1-502, Clone (cell biology), Drug resistance, Biology, Microbiology, ST258, lcsh:Microbiology, 03 medical and health sciences, Genotype, education, Pathogen, Genetics, education.field_of_study, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, dog, Multilocus sequence typing, MRSP, MLST
Abstract: International audience; Staphylococcus pseudintermedius is a colonizer as well as an important pathogen of dogs where it is responsible for skin, ear and post-operative infections. The emergence of methicillin-resistant S. pseudintermedius (MRSP) in the early 2000s, which were additionally resistant to most veterinary-licensed antibiotics, drew specific attention to these pathogens due to the limitations created in veterinary therapeutic options. Multiple studies showed that the sequence type (ST)71 was the most frequently identified clone in Europe. A few years ago, several publications have suggested a decline of the ST71 clone and the emergence of the ST258 lineage in Northern Europe. In this study, we show that ST71 is also decreasing over time in France and that the non-ST71 population is highly heterogeneous. Globally, the non-ST71 clones are more susceptible to antibiotics, which might be good news for veterinarians. Two other lineages, ST258 and ST496, seem to be successful in France. These isolates, as well as representatives of the ST71 clone, underwent whole-genome sequence. This study shows that the ST71 and ST496 clusters are highly homogenous while the ST258 cluster is more diverse. Each ST possesses a specific pattern of resistance and virulence genes. The reasons for the apparent and simultaneous success of the ST258 and ST496 clones remain unclear. But the emergence of the ST496 clone will require monitoring given its multi-resistant genotype and threat to canine health.
Published: 2018

18. Fluorescence-Based Detection of Natural Transformation in Drug-Resistant Acinetobacter baumannii

Author: Marisa Haenni, Anne-Sophie Godeux, Xavier Charpentier, Agnese Lupo, Simon Guette-Marquet, Gottfried Wilharm, Maria-Halima Laaberki, Transfert de gène horizontal chez les bactéries pathogènes – Horizontal gene transfer in bacterial pathogens, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Robert Koch Institute [Berlin] (RKI), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité Antibiorésistance et Virulence Bactériennes, and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
Subjects: 0301 basic medicine, Acinetobacter baumannii, Gene Transfer, Horizontal, medicine.drug_class, 030106 microbiology, Antibiotics, Green Fluorescent Proteins, Drug resistance, Microbial Sensitivity Tests, Microbiology, 03 medical and health sciences, Antibiotic resistance, Bacterial Proteins, Drug Resistance, Multiple, Bacterial, medicine, Molecular Biology, Gene, 2. Zero hunger, Genetics, biology, Acinetobacter, biology.organism_classification, Flow Cytometry, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, DNA-Binding Proteins, 030104 developmental biology, Carbapenems, Microscopy, Fluorescence, Horizontal gene transfer, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Transformation, Bacterial, Bacteria, Acinetobacter Infections
Abstract: Acinetobacter baumannii is a nosocomial agent with a high propensity for developing resistance to antibiotics. This ability relies on horizontal gene transfer mechanisms occurring in the Acinetobacter genus, including natural transformation. To study natural transformation in bacteria, the most prevalent method uses selection for the acquisition of an antibiotic resistance marker in a target chromosomal locus by the recipient cell. Most clinical isolates of A. baumannii are resistant to multiple antibiotics, limiting the use of such selection-based methods. Here, we report the development of a phenotypic and selection-free method based on flow cytometry to detect transformation events in multidrug-resistant (MDR) clinical A. baumannii isolates. To this end, we engineered a translational fusion between the abundant and conserved A. baumannii nucleoprotein (HU) and the superfolder green fluorescent protein (sfGFP). The new method was benchmarked against the conventional antibiotic selection-based method. Using this new method, we investigated several parameters affecting transformation efficiencies and identified conditions of transformability one hundred times higher than those previously reported. Using optimized transformation conditions, we probed natural transformation in a set of MDR clinical and nonclinical animal A. baumannii isolates. Regardless of their origin, the majority of the isolates displayed natural transformability, indicative of a conserved trait in the species. Overall, this new method and optimized protocol will greatly facilitate the study of natural transformation in the opportunistic pathogen A. baumannii. IMPORTANCE Antibiotic resistance is a pressing global health concern with the rise of multiple and panresistant pathogens. The rapid and unfailing resistance to multiple antibiotics of the nosocomial agent Acinetobacter baumannii, notably to carbapenems, prompt to understand the mechanisms behind acquisition of new antibiotic resistance genes. Natural transformation, one of the horizontal gene transfer mechanisms in bacteria, was only recently described in A. baumannii and could explain its ability to acquire resistance genes. We developed a reliable method to probe and study natural transformation mechanism in A. baumannii. More broadly, this new method based on flow cytometry will allow experimental detection and quantification of horizontal gene transfer events in multidrug-resistant A. baumannii.
Published: 2018

19. Epidemic spread of Escherichia coli ST744 isolates carrying mcr-3 and blaCTX-M-55 in cattle in France

Author: Jean-Yves Madec, Racha Beyrouthy, Marisa Haenni, Pierre Châtre, Agnese Lupo, Richard Bonnet, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Faculty of Public Health [Tripoli, Liban] (FSP III), Lebanese University [Beirut], Laboratoire de Lyon, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire d'études et de recherches en pathologie bovine et hygiène des viandes, AFSSA, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Agency for Food, Environmental and Occupational Health and Safety (ANSES), ANR-14-ANWA-0006,PRAHAD,Prevalence and optimised detection of resistance to antibiotics vital for animal and human health(2014), European Project: 323209,EC:FP7:HEALTH,FP7-JPROG-2012-RTD,JPIAMR(2012), Faculty of Public Health [Lebanese University] (FSP III), Lebanese University [Beirut] (LU), Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA), Animal Health and Welfare (ANIHWA) ERA-Net project (France) [ANR-14-ANWA-0006-04], and Joint Programming Initiative on Antimicrobial Resistance (JPI-EC-AMR) project Trans-Comp-ESC-R (France) [JPIAMR2016-077]
Subjects: 0301 basic medicine, Microbiology (medical), Genotype, 030106 microbiology, Cattle Diseases, Transferases (Other Substituted Phosphate Groups), Microbial Sensitivity Tests, Biology, medicine.disease_cause, beta-Lactamases, MESH: Genotype, 03 medical and health sciences, MESH: Anti-Bacterial Agents, Epidemic spread, Drug Resistance, Bacterial, medicine, Escherichia coli, MESH: Cattle Diseases, Animals, Pharmacology (medical), Epidemics, Escherichia coli Infections, ComputingMilieux_MISCELLANEOUS, Pharmacology, Colistin, MESH: Escherichia coli, Escherichia coli Proteins, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Research Letters, 3. Good health, Anti-Bacterial Agents, MESH: France, Infectious Diseases, Cattle, Topography, Medical, MESH: Transferases (Other Substituted Phosphate Groups), France
Abstract: International audience; No abstract available
Published: 2017

20. OXA-48 and CTX-M-15 extended-spectrum beta-lactamases in raw milk in Lebanon: epidemic spread of dominant Klebsiella pneumoniae clones

Author: Estelle Saras, Marisa Haenni, Mohamad Diab, Monzer Hamze, Jean-Yves Madec, Richard Bonnet, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Laboratoire d'études et de recherches en pathologie bovine et hygiène des viandes, AFSSA, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), ANSES, Lebanese University, Social Foundation Azm and Saade, and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Microbiology (medical), CTX-M-15, Klebsiella pneumoniae, 030106 microbiology, MESH: Klebsiella pneumoniae, MESH: beta-Lactamases, medicine.disease_cause, Microbiology, beta-Lactamases, 03 medical and health sciences, carbapenemase, MESH: Anti-Bacterial Agents, Drug Resistance, Multiple, Bacterial, medicine, Pulsed-field gel electrophoresis, polycyclic compounds, Escherichia coli, Animals, MESH: Animals, Typing, MESH: Lebanon, Lebanon, OXA-48, Southern blot, MESH: Gene Expression Regulation, Bacterial, biology, MESH: Escherichia coli, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, MESH: Drug Resistance, Multiple, Bacterial, Gene Expression Regulation, Bacterial, Raw milk, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, bacterial infections and mycoses, Virology, Enterobacteriaceae, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, MESH: Milk, MESH: Cattle, Milk, Multilocus sequence typing, Cattle
Abstract: International audience; Raw milk has recently been reported as a source of extended-spectrum beta-lactamase (ESBL) and carbapenemase genes. We thus investigated the prevalence of ESBL- and carbapenemase-producing Enterobacteriaceae in raw milk in Lebanon in order to assess the risk of transfer of these bacteria to humans. A high prevalence (30.2 %) of CTX-M-15-producing K. pneumoniae was detected in raw bovine milk. Three main K. pneumoniae clones were identified by PFGE and MLST typing. Southern blot experiments revealed that one of these clones carried the blaCTX-M-15 gene chromosomally. Moreover, one OXA-48-producing K. pneumoniae ST530 and seven CTX-M-15-producing Escherichia coli sharing the same ST were also detected. These findings highlight the spread of dominant CTX-M-15-producing K. pneumoniae clones and OXA-48-producing isolates in the food chain. Milk, which is mostly consumed raw in Lebanon, may be a source of human exposure to ESBLs and carbapenemases.
Published: 2017

21. Extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae in water sources in Lebanon

Author: Marisa Haenni, Monzer Hamze, Mohamad Diab, Estelle Saras, Richard Bonnet, Jean-Yves Madec, Université Libanaise, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), French Agency for Food, Environmental and Occupational Health Safety (ANSES), Lebanese University, Azm & Saade Social Foundation, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Laboratoire d'études et de recherches en pathologie bovine et hygiène des viandes, AFSSA, Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], and Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
Subjects: MESH: Water Wells, 0301 basic medicine, Veterinary medicine, Water Wells, medicine.medical_treatment, [SDV]Life Sciences [q-bio], MESH: Klebsiella pneumoniae, Water source, MESH: beta-Lactamases, Drug resistance, carbapenemase, Drug Resistance, Multiple, Bacterial, MESH: Animals, MESH: Bacterial Proteins, well, 2. Zero hunger, Antiinfective agent, MESH: Escherichia coli, General Medicine, Contamination, Enterobacteriaceae, 6. Clean water, Bacterial Typing Techniques, 3. Good health, Klebsiella pneumoniae, MESH: Multilocus Sequence Typing, lebanon, Public Health, Estuaries, Water Microbiology, MESH: Public Health, MESH: Estuaries, DNA, Bacterial, 030106 microbiology, water, MESH: Carbapenem-Resistant Enterobacteriaceae, Biology, Microbiology, beta-Lactamases, MESH: Bacterial Typing Techniques, estuary, MESH: Enterobacteriaceae, MESH: Natural Springs, 03 medical and health sciences, Antibiotic resistance, Bacterial Proteins, Escherichia coli, medicine, Animals, Humans, MESH: Lebanon, spring water, MESH: Humans, General Veterinary, Natural Springs, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Drug Resistance, Multiple, Bacterial, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Water Microbiology, Multiple drug resistance, Carbapenem-Resistant Enterobacteriaceae, 030104 developmental biology, ESBL, Beta-lactamase, Multilocus Sequence Typing
Abstract: International audience; Extended-spectrum beta-lactamases (ESBLs) have been recurrently reported in both human and veterinary medicine, and carbapenemases have also emerged in these two sectors. Such resistance phenotypes were increasingly reported in the environment, which both receives and further disseminates multidrug-resistant (MDR) bacteria. Here, we report the high contamination of water samples (68.2%; 15/22) collected in estuaries in Lebanon. From these 15 contaminated sites, a total of 21 ESBL-producing (mostly harbouring the bla(CTX-M-15) gene) and four carbapenemase-producing (two bla(OXA-48) and two bla(OXA-244)) Enterobacteriaceae were recovered. ESBL contamination was also identified in water samples collected from rural wells and spring water, although at a lower frequency. Indeed, 1.9% (3/155) and 6.1% (7/115) of the wells and springs were contaminated, respectively, and all identified isolates were CTX-M-15-producing E. coli. Interestingly, sequence types (STs) previously associated both with animal and human reservoirs were detected (ST38, ST10 and ST131), suggesting a complex source of contamination. This situation is alarming since water drawn from wells or springs is directly intended for human consumption in Lebanon without any further treatment. Moreover, even though water from estuaries is not intended for human consumption, it is used to water animals and irrigate crops. Consequently, water contamination by ESBLs and carbapenemases in Lebanon is potentially a major risk to public health. Part of this work was presented at the 7th Symposium on Antimicrobial Resistance in Animals and the Environment (ARAE).
Published: 2017

22. Multidrug resistance Salmonella genomic island 1 in a Morganella morganii subsp. morganii human clinical isolate from France

Author: Schultz, Eliette, Barraud, Olivier, Madec, Jean-Yves, Haenni, Marisa, Cloeckaert, Axel, Ploy, Marie-Cécile, Doublet, Benoît, Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), Institut National de la Recherche Agronomique (INRA), Unité Antibiorésistance et Virulence Bactériennes, Laboratoire de Lyon, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de Lyon, Anti-infectieux : supports moléculaires des résistances et innovations thérapeutiques (RESINFIT), CHU Limoges-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), Service de Bactériologie, Virologie, Hygiène [CHU Limoges], CHU Limoges, French National Institute of Agricultural Research, Ministère de l’Enseignement Supérieur et de la Recherche, Institut National de la Santé et de la Recherche Médicale (Inserm), Anses, INRA, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), ProdInra, Archive Ouverte, and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: integrative mobilizable element, Microbiology and Parasitology, Observation, Salmonella genomic island 1, Microbiology, QR1-502, Microbiologie et Parasitologie, Clinical Science and Epidemiology, séquençage du génome, proteus mirabilis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Salmonella genomic island, integrons, multidrug resistance, bacteria, salmonella enterica, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology
Abstract: Since its initial identification in epidemic multidrug-resistant Salmonella enterica serovar Typhimurium DT104 strains, several SGI1 variants, SGI1 lineages, and SGI1-related elements (SGI2, PGI1, and AGI1) have been described in many bacterial genera (Salmonella, Proteus, Morganella, Vibrio, Shewanella, etc.). They constitute a family of multidrug resistance site-specific integrative elements acquired by horizontal gene transfer, SGI1 being the best-characterized element. The horizontal transfer of SGI1/PGI1 elements into other genera is of public health concern, notably with regard to the spread of critically important resistance genes such as ESBL and carbapenemase genes. The identification of SGI1 in Morganella morganii raises the issue of (i) the potential for SGI1 to emerge in other human pathogens and (ii) its bacterial host range. Further surveillance and research are needed to understand the epidemiology, the spread, and the importance of the members of this SGI1 family of integrative elements in contributing to antibiotic resistance development., Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that harbors a great diversity of antimicrobial resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. A serious threat to public health was revealed in the recent description in P. mirabilis of a SGI1-derivative multidrug resistance island named PGI1 (Proteus genomic island 1) carrying extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase resistance genes, blaVEB-6 and blaNDM-1, respectively. Here, we report the first description of Salmonella genomic island 1 (SGI1) in a multidrug-resistant clinical Morganella morganii subsp. morganii strain isolated from a patient in France in 2013. Complete-genome sequencing of the strain revealed SGI1 variant SGI1-L carrying resistance genes dfrA15, floR, tetA(G), blaPSE-1 (now referred to as blaCARB-2), and sul1, conferring resistance to trimethoprim, phenicols, tetracyclines, amoxicillin, and sulfonamides, respectively. The SGI1-L variant was integrated into the usual chromosome-specific integration site at the 3′ end of the trmE gene. Beyond Salmonella enterica and Proteus mirabilis, the SGI1 integrative mobilizable element may thus also disseminate its multidrug resistance phenotype in another genus belonging to the Proteae tribe of the family Enterobacteriaceae. IMPORTANCE Since its initial identification in epidemic multidrug-resistant Salmonella enterica serovar Typhimurium DT104 strains, several SGI1 variants, SGI1 lineages, and SGI1-related elements (SGI2, PGI1, and AGI1) have been described in many bacterial genera (Salmonella, Proteus, Morganella, Vibrio, Shewanella, etc.). They constitute a family of multidrug resistance site-specific integrative elements acquired by horizontal gene transfer, SGI1 being the best-characterized element. The horizontal transfer of SGI1/PGI1 elements into other genera is of public health concern, notably with regard to the spread of critically important resistance genes such as ESBL and carbapenemase genes. The identification of SGI1 in Morganella morganii raises the issue of (i) the potential for SGI1 to emerge in other human pathogens and (ii) its bacterial host range. Further surveillance and research are needed to understand the epidemiology, the spread, and the importance of the members of this SGI1 family of integrative elements in contributing to antibiotic resistance development.
Published: 2017

23. Impact of food animal trade on the spread of mcr-1-mediated colistin resistance, Tunisia, July 2015

Author: Olfa Bouallegue, Wejdene Mansour, Wahib Mehri, Noureddine Boujaâfar, Marisa Haenni, Raoudha Grami, Jean-Yves Madec, Hôpital Universitaire Sahloul (CHU Sahloul), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut Supérieur des Sciences Appliquées et de Technologie de Mahdia, Commissariat Régional au Développement Agricole, Ministère de l'agriculture, and European Project: 291815,EC:FP7:KBBE,FP7-ERANET-2011-RTD,ANIHWA(2012)
Subjects: 0301 basic medicine, Veterinary medicine, animal structures, Meat, Tunisia, Genotype, Epidemiology, Food animal, 030106 microbiology, Microbial Sensitivity Tests, Biology, beta-Lactamases, Colistin resistance, 03 medical and health sciences, Virology, Drug Resistance, Bacterial, medicine, Escherichia coli, Prevalence, Animals, Humans, Escherichia coli Infections, business.industry, Colistin, Public Health, Environmental and Occupational Health, Commerce, Food sample, Poultry farming, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, Food Microbiology, MCR-1, France, business, Peptides, Chickens, medicine.drug, Plasmids
Abstract: We report a high prevalence of MCR-1 and CTX-M-1-producing Escherichia coli in three Tunisian chicken farms. Chickens were imported from France or derived from French imported chicks. The same IncHI2-type plasmid reported to carry those genes in cattle in France and in a food sample in Portugal was found in Tunisian chickens of French origin. This suggests a significant impact of food animal trade on the spread of mcr-1-mediated colistin resistance in Europe.
Published: 2016

24. Divergent evolution of the repFII replicon of incF plasmids carrying cytotoxic necrotizing factor cnf2, cytolethal distending toxin cdtIII, and f17Ae fimbrial variant genes in type 2 necrotoxigenic escherichia coli isolates from calves

Author: Bihannic, Morgan, Haenni, Marisa, Oswald, Eric, Madec, Jean-Yves, Centre de Physiopathologie de Toulouse-Purpan (INSERM U563 - CNRS UMR1037), Centre National de la Recherche Scientifique (CNRS)-Centre de lutte contre le cancer (CLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Institut Claudius Regaud, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre Hospitalier Universitaire de Purpan (CHU Purpan), French Agency for Food, Environmental and Occupational Health and Safety (Anses), Institut National de la Recherche Agronomique (INRA), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut Claudius Regaud-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de lutte contre le cancer (CLCC)-Centre National de la Recherche Scientifique (CNRS), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and ProdInra, Migration
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: International audience; Among the pathovars of Escherichia coli in cattle, necrotoxigenic E. coli (NTEC) is defined by the production of cytotoxic necrotizing factors (CNFs). In particular, type 2 NTEC (NTEC2) strains are frequent in diarrheic and septicemic calves and usually coproduce CNF type 2 (CNF2), cytolethal distending toxin type III (CDTIII), and fimbrial adhesins of the F17 family, whose genetic determinants have frequently been reported on the same Vir-like plasmid. In this study, we investigated the genetic environment of the cnf2, f17Ae, and cdtIII genes in a collection of fecal E. coli isolates recovered from 484 French and 58 Iranian calves. In particular, we highlighted the spread of cnf2, f17Ae, and cdtIII on similar 150-kb IncF plasmids harboring the newly assigned repFII replicon allele F74 in NTEC2 isolates. Interestingly, this 150-kb IncF plasmid differed from the 140-kb IncF plasmid harboring the newly assigned repFII replicon allele F75 and carrying cnf2 alone. These results suggest two divergent lineages of cnf2-carrying IncF plasmids depending on the presence of the f17Ae and cdtIII genes. This partition was observed in E. coli strains of unrelated backgrounds, suggesting two different evolutionary paths of cnf2-carrying IncF plasmids rather than divergent evolutions of NTEC2 clones. The driving forces for such divergent evolutions are not known, and further studies are required to clarify the selection of plasmid subtypes spreading virulence determinants in E. coli, in particular, plasmids of the IncF family.
Published: 2016

25. Non-ST131 Escherichia coli from cattle harbouring human-like blaCTX-M-15-carrying plasmids

Author: Aurore Gourguechon, Patrice Nordmann, Jean-Yves Madec, Estelle Saras, Laurent Poirel, Marisa Haenni, Delphine Girlich, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Résistances émergentes aux antibiotiques, Institut National de la Santé et de la Recherche Médicale (INSERM), European Project: 223031,EC:FP7:HEALTH,FP7-HEALTH-2007-B,TROCAR(2009), and European Project: 241742,EC:FP7:HEALTH,FP7-HEALTH-2009-single-stage,TEMPOTEST-QC(2010)
Subjects: Microbiology (medical), Genotype, Virulence, Cattle Diseases, Microbial Sensitivity Tests, Biology, medicine.disease_cause, Polymerase Chain Reaction, beta-Lactamases, 03 medical and health sciences, Feces, Plasmid, medicine, Escherichia coli, Animals, Cluster Analysis, Humans, Pharmacology (medical), Typing, Replicon, Escherichia coli Infections, Phylogeny, 030304 developmental biology, 2. Zero hunger, Pharmacology, Genetics, 0303 health sciences, 030306 microbiology, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, Electrophoresis, Gel, Pulsed-Field, Molecular Typing, Infectious Diseases, Multilocus sequence typing, Cattle, Restriction fragment length polymorphism, Polymorphism, Restriction Fragment Length, Plasmids
Abstract: Objectives To characterize bla(CTX-M-15)-carrying plasmids and lineages of nine strains of Escherichia coli from cattle. Methods Plasmid DNA was analysed using PCR-based replicon typing and plasmid sub-typing schemes, restriction fragment length polymorphism, S1 nuclease-PFGE and Southern hybridization. Strains were characterized by PFGE, multilocus sequence typing, phylogenetic grouping and B2-O25b:H4-ST131 (where ST stands for sequence type) clone screening. Susceptibilities to antimicrobials were determined by agar diffusion and resistance genes were characterized by PCR and sequencing. Results The bla(CTX-M-15) gene was found on F31:A4:B1/IncFII and F2:A-:B-/IncFII plasmids, which have been reported abundantly in humans. On F31:A4:B1/IncFII plasmids, the bla(CTX-M-15) gene was associated with the bla(TEM-1), bla(OXA-1) and aac(6')-Ib-cr resistance genes. The bla(CTX-M-15) gene was also found on IncI1 plasmids of the CC31 clonal complex, recently identified in the human epidemic and virulent E. coli clone O104:H4. None of the cattle isolates belonged to the human and widespread clone B2-O25b:H4/ST131, but were mostly of new STs and of the phylogenetic groups A (n=4), B1 (n=3) or D (n=2). The E. coli isolates harbouring the bla(CTX-M-15)-carrying plasmids were genetically diverse, and were recovered from different geographical locations and farms and at different times. Conclusions This study demonstrates that bla(CTX-M-15)-carrying plasmids from cattle-derived non-ST131 E. coli isolates were highly similar to those found in ST131 E. coli isolates commonly reported in humans. It also exemplifies the key role of plasmids versus clonal dissemination in the spread of the bla(CTX-M-15) gene among cattle, and possibly between E. coli isolates detected in humans and cattle.
Published: 2011
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26. Geographical clustering of mecC-positive Staphylococcus aureus from bovine mastitis in France

Author: Pierre Châtre, Marisa Haenni, Nathalie Nowak, Jean-Yves Madec, Jason Tasse, Frédéric Laurent, Michèle Bes, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, Laboratoire véterinaire et Alimentaire Départemental de Meurthe et Moselle, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), Staphylococcus aureus, Biology, medicine.disease_cause, Microbiology, Bacterial Proteins, medicine, Animals, Penicillin-Binding Proteins, Pharmacology (medical), Cluster analysis, Mastitis, Bovine, ComputingMilieux_MISCELLANEOUS, Pharmacology, Staphylococcal Infections, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Mastitis, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Cattle, Female, France
Abstract: International audience
Published: 2014

27. Assessment of Adhesins as an Indicator of Pathovar-Associated Virulence Factors in Bovine Escherichia coli

Author: Charlotte Valat, Karine Forest, Frédéric Auvray, Véronique Métayer, Thomas Méheut, Charlène Polizzi, Emilie Gay, Marisa Haenni, Eric Oswald, Jean-Yves Madec, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Paris-Est (UPE), Unité Epidémiologie, Centre de Physiopathologie de Toulouse-Purpan (INSERM U563 - CNRS UMR1037), Centre National de la Recherche Scientifique (CNRS)-Centre de lutte contre le cancer (CLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Institut Claudius Regaud, Centre Hospitalier Universitaire de Purpan (CHU Purpan), ProdInra, Migration, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut Claudius Regaud-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de lutte contre le cancer (CLCC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genotype, Virulence Factors, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Virulence, Cattle Diseases, medicine.disease_cause, Serogroup, Applied Microbiology and Biotechnology, Virulence factor, Microbiology, Serology, Enteritis, 03 medical and health sciences, Pathogenic Escherichia coli, Drug Resistance, Bacterial, medicine, Escherichia coli, Animals, Adhesins, Bacterial, Escherichia coli Infections, 030304 developmental biology, 0303 health sciences, Ecology, biology, 030306 microbiology, Public and Environmental Health Microbiology, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, medicine.disease, Bacterial adhesin, [SDV] Life Sciences [q-bio], Pathovar, Cattle, Food Science, Biotechnology
Abstract: The CS31A, F17, and F5 adhesins are usually targeted by serology-based methods to detect pathogenic Escherichia coli associated with calf enteritis. However, the virulence traits of the selected isolates are still poorly described. Here, from a set of 349 diarrheagenic E. coli isolates from cattle, we demonstrated a 70.8% concordance rate (Cohen's kappa, 0.599) between serology- and PCR-based approaches for the detection of adhesins under field conditions. A 79% to 82.4% correspondence between the two methods was found for fimbrial adhesins, whereas major discrepancies (33%) were observed for CS31A-type antigens. Various F17A variants were found, such as F17Ac (20K) (50%), F17Aa (FY) (18.9%), F17Ab (8.1%), and F17Ad (111K) (5.4%), including a high proportion (17.6%) of new F17A internal combinations (F17Aab, F17Aac, and F17Abc) or untypeable variants. In addition, the highest proportion of pathovar-associated virulence factor (VF) genes was observed among E. coli isolates that produced F5/F41 adhesins. A specific link between the heat-stable toxins related to the enterotoxigenic E. coli (ETEC) pathovar and adhesins was identified. STa was significantly linked to F5/F41 and EAST1 to CS31A adhesins ( P < 0.001), respectively, whereas NTEC was associated with F17 adhesin ( P = 0.001). Clustering between phylogroups according to the adhesin types was also observed. Also, few Shiga toxin-producing E. coli (STEC) or enteropathogenic E. coli (EPEC) pathovars were identified. Finally, no statistically significant difference was observed in the occurrence of extended-spectrum beta lactamase (ESBL) production according to the adhesins expressed by the isolates ( P = 0.09). Altogether, this study gives new insights into the relationship between adhesins, VF, and antimicrobial resistance in calf enteritis and supports the need for further standardization of methodologies for such approaches.
Published: 2014

28. Identification and detection of three new F17 fimbrial variants in Escherichia coli strains isolated from cattle

Author: Reza Ghanbarpour, Morgan Bihannic, Frédéric Auvray, Pierre Châtre, Michèle Boury, Hubert Brugère, Laurent Cavalié, Eric Oswald, Jean-Yves Madec, Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Microbiology Department, Shahid Bahonar University of Kerman, Unité Ecophysiologie et Détection Bactérienne, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Service Bactériologie et hygiène [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), This work was supported by Institut National de la Recherche Agronomique(INRA). Morgan Bihannic had a PhD fellowship from the Institut National dela Recherche Agronomique (INRA) and the French Agency for Food,Environmental and Occupational Health and Safety (Anses). We gratefullythank Patricia Martin for helpful discussions and proofreading., Taibi, Nadia, Madec, Jean-Yves, Unité Antibiorésistance et Virulence Bactériennes, Service de Bactériologie-Hygiène, CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], Institut National de la Recherche Agronomique (INRA), and French Agency for Food, Environmental and Occupational Health and Safety (Anses)
Subjects: Diarrhea, [SDV]Life Sciences [q-bio], Population, Molecular Sequence Data, diarrhée, Virulence, Cattle Diseases, medicine.disease_cause, Polymerase Chain Reaction, Microbiology, Pathogenic Escherichia coli, Gene cluster, medicine, Animals, education, Escherichia coli, Escherichia coli Infections, Phylogeny, virulence bactérienne, education.field_of_study, Adhesins, Escherichia coli, septicemie, General Veterinary, biology, Base Sequence, Research, Escherichia coli Proteins, veau, toxine bactérienne, agneau, biology.organism_classification, Pathogenicity island, veterinary(all), variation génétique, 3. Good health, facteur de pathogénicité, Bacterial adhesin, Médecine vétérinaire et santé animal, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Pilin, Fimbriae, Bacterial, biology.protein, protéine pathogène, Cattle, Veterinary medicine and animal Health, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, escherichia coli, bactérie pathogène, expression des gènes
Abstract: International audience; F17 fimbriae are produced by pathogenic Escherichia coli involved in diarrhea and septicemia outbreaks in calves and lambs. These proteins result from the expression of four different clustered genes, namely f17A, f17D, f17C and f17G, encoding a pilin protein, a periplasmic protein, an anchor protein and an adhesin protein, respectively. Several variants of f17A and f17G genes have been reported and found genetically associated with typical virulence factors of bovine pathogenic E. coli strains. In this study, a new F17e-A variant, closely related to F17b-A, was identified from a collection of 58 E. coli isolates from diarrheic calves in Iran. While highly prevalent in Iranian F17-producing clinical isolates from calves, this variant was rare among E. coli from a French healthy adult bovine population, suggesting a possible association with virulence. The f17Ae gene was also found in the genome of the Shiga-like toxin variant Stx1d–producing bovine E. coli strain MHI813, and belonged to a gene cluster also encoding a new F17-G3 variant, which greatly differed from F17-G1 and F17-G2. This gene cluster was located on a pathogenicity island integrated in the tRNA pheV gene. The gene coding for a third new F17f-A variant corresponding to a combination of F17c-A and F17d-A was also identified on the pVir68 plasmid in the bovine pathogenic E. coli strain 6.0900. In conclusion, we identified three new F17-A and F17-G variants in cattle E. coli, which may also have significant impact on the development of new diagnostics and vaccination tools.
Published: 2013

29. Comparative phylogenomics of ESBL-, AmpC- and carbapenemase-producing Klebsiella pneumoniae originating from companion animals and humans

Author: Garcia-Fierro, Raquel, Drapeau, Antoine, Dazas, Melody, Saras, Estelle, Rodrigues, Carla, Brisse, Sylvain, Madec, Jean-Yves, Haenni, Marisa, Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), and European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health)(2018)
Subjects: Klebsiella pneumoniae, Carbapenem-Resistant Enterobacteriaceae, Bacterial Proteins, Animals, Humans, Pets, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Phylogeny, beta-Lactamases, Klebsiella Infections
Abstract: Background:WHO considers ESBL- and carbapenemase-producingKlebsiella pneumoniaea major global concern. In animals, ESBL- and carbapenemase-producingK. pneumoniaeof human-related ST11, ST15 and ST307 have been reported, but not in the context of large WGS-based One Health investigations. Objectives:To perform comparative phylogenomics on a large collection of multidrug-resistant (MDR)K. pneumoniaerecovered from diseased companion animals and humans. Methods:MDRK. pneumoniae(n=105) recovered from companion animals in France during 2010–18 were phenotypically characterized. All isolates were whole-genome sequenced using the NovaSeq technology and phylogenomic analysis across animal and humanK. pneumoniaewas performed using appropriate pipelines. Results:blaCTX-M-15,blaDHA-1andblaOXA-48were strongly associated with IncFIIk, IncR and IncL plasmids, re- spectively. When compared with humanK. pneumoniaegenomes, four groups of closely related French human and animal isolates belonging to ST11, ST15 and ST307 were detected, suggesting the circulation of clones between the human and animal sectors at country level. A large cluster of 31 ST11-KL105 animal isolates from France and Switzerland suggested it corresponds to a sub-lineage that is particularly well-adapted to the animal host. Conclusions:This study demonstrates the spread ofblaCTX-M-15-carrying ST15 and ST307, andblaDHA-1-carrying ST11K. pneumoniaeclones in animal populations. ST11 was the main vector ofblaOXA-48/IncL, despite the absence of carbapenem use in French animals. Comparative phylogenomics suggests cross-transmission ofK. pneumoniaesub-lineages more prone than others to colonize/infect the animal host. Our data also evidenced the emergence of convergent hypervirulent and MDRK. pneumoniaein animals.
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30. An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes.

Author: Rochegüe T, Haenni M, Cazeau G, Metayer V, Madec JY, Ferry T, and Lupo A
Subjects: Gene Expression Regulation, Bacterial, Hydrolysis, RNA, Ribosomal, 16S, Real-Time Polymerase Chain Reaction, beta-Lactamases genetics, beta-Lactamases metabolism, Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial genetics, Enterobacteriaceae drug effects
Abstract: Early antibiotic resistance determinants (ARDs) detection in humans or animals is crucial to counteract their propagation. The ARDs quantification is fundamental to understand the perturbation caused by disruptors, such as antibiotics, during therapies. Forty-three qPCRs on the most diffused ARDs and integrons among human and animal Enterobacterales, and one on the 16S rDNA for bacteria quantification, were developed. The qPCRs, using hydrolysis probes, operated with a unique amplification condition and were tested analytically and diagnostically performing 435 reactions on five positive and negative controls for each qPCR. Diagnostic sensitivity and specificity were confirmed by PCR and genome sequencing of control isolates, demonstrating 100% performance for all qPCRs. An easy and rapid discrimination method for the epidemiologically relevant bla CTX-Ms is provided. This large, noncommercial qPCRs inventory could serve for precise quantification of ARDs, but also as a rapid screening tool for surveillance purposes, providing the basis for further high-throughput developments., (Copyright © 2021 Elsevier Inc. All rights reserved.)
Published: 2021
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31. Development and Multicentric Validation of a Lateral Flow Immunoassay for Rapid Detection of MCR-1-Producing Enterobacteriaceae .

Author: Volland H, Dortet L, Bernabeu S, Boutal H, Haenni M, Madec JY, Robin F, Beyrouthy R, Naas T, and Simon S
Subjects: Animals, Anti-Bacterial Agents pharmacology, Bacterial Proteins analysis, Colistin pharmacology, Drug Resistance, Bacterial, Enterobacteriaceae enzymology, Enterobacteriaceae Infections microbiology, Humans, Microbial Sensitivity Tests, Plasmids genetics, Capillary Action, Enterobacteriaceae isolation & purification, Escherichia coli Proteins analysis, Immunoassay
Abstract: Colistin has become a last-resort antibiotic for the treatment of infections caused by highly drug-resistant Gram-negative bacteria. Moreover, it has been widely used in the livestock sector. As a consequence, colistin resistance is emerging worldwide. Among the colistin resistance mechanisms, the spread of the plasmid-encoded colistin resistance gene mcr-1 (mostly in Escherichia coli ) is of particular concern due to its increased transferability compared to that of chromosome-encoded resistance. The early detection of MCR-1-producing bacteria is essential to prevent further spread and provide appropriate antimicrobial therapy. Lateral flow immunoassays (LFIAs) were manufactured with selected monoclonal antibodies. A collection of 177 human and 121 animal enterobacterial isolates was tested in a multicentric study. One bacterial colony grown on agar plates was suspended in extraction buffer and dispensed on the cassette. Migration was allowed for 15 min, and the results were monitored by the appearance of a specific band. The positive results showed a pink line resulting in an unambiguous interpretation. All MCR-1-producing isolates were found to be positive by the LFIA, and no false-negative results were observed. Three out of four MCR-2-producing isolates were also found to be positive. Our test does not detect MCR-3-, MCR-4-, or MCR-5-producing isolates. LFIA allows the detection of MCR-1 with 100% sensitivity and 98% specificity. This test is fast, sensitive, specific, easy to use, and cost-effective and can therefore be implemented in any microbiology laboratory worldwide. LFIA is a major tool for the rapid detection and monitoring of MCR-1 producers in humans and animals., (Copyright © 2019 Volland et al.)
Published: 2019
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31 results on '"Unité Antibiorésistance et Virulence Bactériennes (AVB)"'

1. Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America

2. High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods

3. Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance

4. Interplay between Bacterial Clones and Plasmids in the Spread of Antibiotic Resistance Genes in the Gut: Lessons from a Temporal Study in Veal Calves

5. Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota

6. Host Colonization as a Major Evolutionary Force Favoring the Diversity and the Emergence of the Worldwide Multidrug-Resistant Escherichia coli ST131

7. Drivers of ESBL-producing Escherichia coli dynamics in calf fattening farms: A modelling study

8. Comparison of Phenotypical Antimicrobial Resistance between Clinical and Non-Clinical E. coli Isolates from Broilers, Turkeys and Calves in Four European Countries

9. Characterization of cultivable airborne bacteria and their antimicrobial resistance pattern in French milking parlour

10. Horsing around : Escherichia coli ST1250 of equine origin harboring epidemic IncHI1/ST9 plasmid with blaCTX-M-1and an operon for short-chain fructooligosaccharide metabolism

11. Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli

12. Temporal dynamics of the fecal microbiota in veal calves in a 6-month field trial

13. A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales

14. Scarless Removal of Large Resistance Island AbaR Results in Antibiotic Susceptibility and Increased Natural Transformability in Acinetobacter baumannii

15. An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes

16. Persistence and Diffusion of mecC-Positive CC130 MRSA Isolates in Dairy Farms in Meurthe-et-Moselle County (France)

17. Evolution of the Population Structure of Staphylococcus pseudintermedius in France

18. Fluorescence-Based Detection of Natural Transformation in Drug-Resistant Acinetobacter baumannii

19. Epidemic spread of Escherichia coli ST744 isolates carrying mcr-3 and blaCTX-M-55 in cattle in France

20. OXA-48 and CTX-M-15 extended-spectrum beta-lactamases in raw milk in Lebanon: epidemic spread of dominant Klebsiella pneumoniae clones

21. Extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae in water sources in Lebanon

22. Multidrug resistance Salmonella genomic island 1 in a Morganella morganii subsp. morganii human clinical isolate from France

23. Impact of food animal trade on the spread of mcr-1-mediated colistin resistance, Tunisia, July 2015

24. Divergent evolution of the repFII replicon of incF plasmids carrying cytotoxic necrotizing factor cnf2, cytolethal distending toxin cdtIII, and f17Ae fimbrial variant genes in type 2 necrotoxigenic escherichia coli isolates from calves

25. Non-ST131 Escherichia coli from cattle harbouring human-like blaCTX-M-15-carrying plasmids

26. Geographical clustering of mecC-positive Staphylococcus aureus from bovine mastitis in France

27. Assessment of Adhesins as an Indicator of Pathovar-Associated Virulence Factors in Bovine Escherichia coli

28. Identification and detection of three new F17 fimbrial variants in Escherichia coli strains isolated from cattle

29. Comparative phylogenomics of ESBL-, AmpC- and carbapenemase-producing Klebsiella pneumoniae originating from companion animals and humans

30. An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes.

31. Development and Multicentric Validation of a Lateral Flow Immunoassay for Rapid Detection of MCR-1-Producing Enterobacteriaceae .

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